The research focused on analyzing the UGT gene family in Cannabis sativa, which plays a crucial role in the plant\'s metabolism and glycosylation of secondary metabolites. The study identified 125 UGTs using conserved plant secondary product glycosyltransferase (PSPG) motif amino acid sequences. These UGT genes were categorized into 17 groups (A-Q) through phylogenetic analysis, showing their distribution across 10 chromosomes in C. sativa. The expansion of the CsUGT gene family was attributed to tandem and duplication events, as suggested by gene duplication analysis. Furthermore, the study found various cis-acting regulatory elements related to phytohormones and stress responses in CsUGT promoter regions. Subcellular localization analysis revealed that CsUGT is present in the cytoplasm, chloroplast, and nucleus. The study revealed that CsUGT plays a significant role in various biological processes, cellular components, and molecular functions as highlighted by Gene Ontology analysis. Additionally, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that some CsUGTs are associated with the biosynthesis of secondary metabolites. This research provides valuable insights into the genomic organization, evolutionary history, and potential regulatory mechanisms of UGT genes in C. sativa. It lays the foundation for further exploration of their specific biological roles and potential applications in the plant\'s metabolism and stress responses. These findings contribute to a better understanding of the UGT gene family and its relevance to the metabolic pathways in C. sativa.
UNASSIGNED: The online version contains supplementary material available at 10.1007/s13205-024-04025-3.

Background In addition to genetic predisposition, occupational and environmental factors are important for the risk of prostate cancer. We investigated the effect of single nucleotide polymorphisms (SNPs) on the development of prostate cancer in Japan, including occupational and industrial history as confounding factors in addition to age, smoking, and alcohol drinking. Methods We enrolled 210 prostate cancer patients and 504 male control patients. We conducted four genome-wide association study (GWAS) patterns for prostate cancer development. In the association test, logistic regression models incorporated age, smoking history, alcohol consumption history, and each pattern of industrial/occupational classification. Results No SNPs satisfying the genome-wide significance level of 5×10-8 were detected in GWAS. SNPs with a suggestive association level of 1×10-6 were found near the long intergenic non-protein coding RNA 1824 (LINC01824) and tripartite motif family like 2 (TRIML2) genes in the GWAS using occupational history as a confounder and near the ribosomal protein S2 pseudogene 25 (RPS2P25) gene in the GWAS using industrial history as a confounder. No SNPs that met the suggestive association level were observed in the GWAS that did not include occupational and industrial history. Conclusion By adding occupational and industrial history to the confounding factors, there were SNPs detected in the GWAS for prostate cancer development. The consideration of occupational and industrial history may increase the usefulness of GWAS.

Most studies have focused on the risk factors, treatment, and care of affective psychosis, and several have reported a relationship between ambient air quality and this psychosis. Although an association has been reported between psychosis and genes, studies mainly explored the associations between one type of psychosis and one gene; few have identified genes related to affective psychosis. This study investigates the genetic and environmental factors of affective psychosis.
In this retrospective longitudinal study, 27 604 participants aged 30-70 were selected from Taiwan Biobank. The participants\' propensity scores were calculated based on their demographic information, and propensity score matching was performed to divide the participants into an experimental (i.e., affective psychosis) and control group at a 1:5 ratio. Plink was used to analyze the major and minor types of gene expression related to affective psychosis, and PM2.5 exposure was incorporated into the analyses.
According to the generalized estimating equation analysis results, 8 single nucleotide polymorphisms (SNPs) belonging to the ANK3, BDNF, CACNA1C, and GRID1 genotypes were significantly correlated with depressive disorder (P < .001), with the majority belonging to the ANK3 and CACNA1C. A total of 5 SNPs belonging to the CACNA1C, GRID1, and SIRT1 genotypes were significantly correlated with bipolar disorder (P < .001), with the majority belonging to the CACNA1C. No significant correlation was identified between ambient air pollution and affective psychosis.
CACNA1C and GRID1 are common SNP genotypes for depressive disorder and bipolar disorder and should be considered associated with affective psychosis.

1. This study measured six reproduction traits in a Sichuan white goose population (209 individuals), including fertility, qualified egg rate, plasma concentrations of progesterone (P), follicle-stimulating hormone (FSH), prolactin (PRL) and oestrogen (E2).2. Whole-genome resequencing data from the same goose population (209 individuals) were used in a genome-wide association study (GWAS) utilising a mixed linear model to investigate the genes and genetic markers associated with reproduction traits. The frequency of the selected SNPs and haplotypes were determined using the Matrix-Assisted Laser Desorption Ionisation Time-Of-Flight Mass Spectrometry (MALDI-TOF MS) method.3. In total, 42 SNPs significantly associated with these traits were identified. A haplotype block was constructed based on five SNPs that were significantly associated with qualified egg rate, with individuals having the haplotype CCTTAAGGAA having the lowest qualified egg rate.4. In conclusion, these results provided potential markers for marker-assisted selection to improve goose reproductive performance and a basis for elucidating the genetics of goose reproduction.

In the TRIDENT-2 study, all pregnant women in the Netherlands are offered genome-wide non-invasive prenatal testing (GW-NIPT) with a choice of receiving either full screening or screening solely for common trisomies. Previous data showed that GW-NIPT can reliably detect common trisomies in the general obstetric population and that this test can also detect other chromosomal abnormalities (additional findings). However, evidence regarding the clinical impact of screening for additional findings is lacking. Therefore, we present follow-up results of the TRIDENT-2 study to determine this clinical impact based on the laboratory and perinatal outcomes of cases with additional findings. Between April 2017 and April 2019, additional findings were detected in 402/110,739 pregnancies (0.36%). For 358 cases, the origin was proven to be either fetal (n = 79; 22.1%), (assumed) confined placental mosaicism (CPM) (n = 189; 52.8%), or maternal (n = 90; 25.1%). For the remaining 44 (10.9%), the origin of the aberration could not be determined. Most fetal chromosomal aberrations were pathogenic and associated with severe clinical phenotypes (61/79; 77.2%). For CPM cases, occurrence of pre-eclampsia (8.5% [16/189] vs 0.5% [754/159,924]; RR 18.5), and birth weight <2.3rd percentile (13.6% [24/177] vs 2.5% [3,892/155,491]; RR 5.5) were significantly increased compared to the general obstetric population. Of the 90 maternal findings, 12 (13.3%) were malignancies and 32 (35.6%) (mosaic) pathogenic copy number variants, mostly associated with mild or no clinical phenotypes. Data from this large cohort study provide crucial information for deciding if and how to implement GW-NIPT in screening programs. Additionally, these data can inform the challenging interpretation, counseling, and follow-up of additional findings.

This study examined the effects of single-nucleotide polymorphisms (SNPs) on the development of bladder cancer, adding longest-held occupational and industrial history as regulators. The genome purified from blood was genotyped, followed by SNP imputation. In the genome-wide association study (GWAS), several patterns of industrial/occupational classifications were added to logistic regression models. The association test between bladder cancer development and the calculated genetic score for each gene region was evaluated (gene-wise analysis). In the GWAS and gene-wise analysis, the gliomedin gene satisfied both suggestive association levels of 10-5 in the GWAS and 10-4 in the gene-wise analysis for male bladder cancer. The expression of the gliomedin protein in the nucleus of bladder cancer cells decreased in cancers with a tendency to infiltrate and those with strong cell atypia. It is hypothesized that gliomedin is involved in the development of bladder cancer.

COVID-19 has posed unforeseen circumstances and throttled major economies worldwide. India has witnessed two waves affecting around 31 million people representing 16% of the cases globally. To date, the epidemic waves have not been comprehensively investigated to understand pandemic progress in India.
Here, we aim for pan Indian cross-sectional evolutionary analysis since inception of SARS-CoV-2.
High quality genomes, along with their collection date till 26th July 2021, were downloaded. Whole genome-based phylogeny was obtained. Further, the mutational analysis was performed using SARS-CoV-2 first reported from Wuhan (NC_045512.2) as reference.
Based on reported cases and mutation rates, we could divide the Indian epidemic into seven phases. The average mutation rate for the pre-first wave was <11, which elevated to 17 in the first wave and doubled in the second wave (∼34). In accordance with mutation rate, VOCs and VOIs started appearing in the first wave (1.5%), which dominated the second (∼96%) and post-second wave (100%). Nation-wide mutational analysis depicted >0.5 million mutation events with four major mutations in >19,300 genomes, including two mutations in coding (spike (D614G), and NSP 12b (P314L) of rdrp), one silent mutation (NSP3 F106F) and one extragenic mutation (5\' UTR 241).
Whole genome-based phylogeny could demarcate post-first wave isolates from previous ones by point of diversification leading to incidences of VOCs and VOIs in India. Such analysis is crucial in the timely management of pandemic.

BACKGROUND: Cranial radiation therapy (CRT) is associated with ototoxicity, which manifests as hearing loss and tinnitus. The authors sought to identify clinical determinants and genetic risk factors for ototoxicity among adult survivors of pediatric cancer treated with CRT.
METHODS: Logistic regression evaluated associations of tinnitus (n = 1991) and hearing loss (n = 2198) with nongenetic risk factors and comorbidities among CRT-treated survivors in the Childhood Cancer Survivor Study. Genome-wide association studies (GWASs) of CRT-related tinnitus and hearing loss were also performed.
RESULTS: Males were more likely to report CRT-related tinnitus (9.4% vs 5.4%; P = 5.1 × 10-4 ) and hearing loss (14.0% vs 10.7%; P = .02) than females. Survivors with tinnitus or hearing loss were more likely to experience persistent dizziness or vertigo (tinnitus: P < 2 × 10-16 ; hearing loss: P = 6.4 × 10-9 ), take antidepressants (tinnitus: P = .02; hearing loss: P = .01), and report poorer overall health (tinnitus: P = 1.5 × 10-6 ; hearing loss: P = 1.7 × 10-6 ) in comparison with controls. GWAS of CRT-related tinnitus revealed a genome-wide significant signal in chromosome 1 led by rs203248 (P = 1.5 × 10-9 ), whereas GWAS of CRT-related hearing loss identified rs332013 (P = 5.8 × 10-7 ) in chromosome 8 and rs67522722 (P = 7.8 × 10-7 ) in chromosome 6 as nearly genome-wide significant. A replication analysis identified rs67522722, intronic to ATXN1, as being significantly associated with CRT-related hearing loss (P = .03) and de novo hearing loss (P = 3.6 × 10-4 ).
CONCLUSIONS: CRT-associated ototoxicity was associated with sex, several neuro-otological symptoms, increased antidepressant use, and poorer self-reported health. GWAS of CRT-related hearing loss identified rs67522722, which was supported in an independent cohort of survivors.
UNASSIGNED: Hearing loss and subjective tinnitus (the perception of noise or ringing in the ear) are long-term side effects of cancer treatment and are common in children treated with radiation to the brain. These toxicities can affect childhood development and potentially contribute to serious learning and behavioral difficulties. This study\'s data indicate that males are at greater risk for hearing loss and tinnitus than females after radiation therapy to the brain. Those who develop these toxicities are more likely to use antidepressants and report poorer overall health. Health care providers can improve the management of survivors by informing patients and/or their parents of these risks.

Over 9.5 million Latinos could be affected by cataracts by 2050. However, no known cataract genetic risk alleles have been identified in Latinos. Moreover, no mitochondrial genome-wide association studies (MiWAS) have been conducted on cataracts in a Latino cohort despite the association between mitochondrial dysfunction and cataracts. Our purpose was to identify a mitochondrial DNA variant that associated with cataracts in a large-scale Latino population.
We conducted an MiWAS to identify mitochondrial single-nucleotide polymorphisms that modify cataract risk in nearly 3500 individuals enrolled in the Los Angles Latino Eye Study cohort, the largest Latino-specific cohort with comprehensive cataract data. Our analytic strategy for MiWAS included logistic regression on cataract occurrence while controlling for mitochondrial genetic ancestry, age, and biological sex.
We found that MitoG228A (rs41323649) alternative allele carriers experienced a five times greater risk for cataracts compared with reference allele carriers. Alternative allele carriers also developed cataracts earlier in life compared with reference allele carriers. Intracohort cross-validation with 10-fold resampling and five repeats showed that the effect of MitoG228A remained significant.
MitoG228A increased risk for cataracts five-fold in approximately 3500 Latinos. To the best of our knowledge, this is the first cataract MiWAS on a large-scale Latino population. This association needs to be validated in an independent cohort.
Our discovery hypothesis-generating study suggest MitoG228A has potential to be used as a risk factor in the clinic and as a target for therapeutics. With validation via an independent cohort, MitoG228A could be used to estimate cataract risk for a Latino to reduce complications later in life.

Aim: To investigate DNA methylation changes in placenta tissues associated with small for gestational age (SGA). Materials & methods: A prospective cohort study consisting of 1292 pregnant women from China (including 39 SGA with placenta tissues) was performed, microarray and pyrosequencing were conducted. Results: Total 2012 methylation variable positions stood out from all probes (p < 0.05; Δβ > 0.2). In SGA cases, a CpG site within ANKRD20B showed lower methylation level (p = 0.032) than appropriate for gestational age in validation cohort. Five sites within FAM198A (p = 0.047, 0.050, 0.039, 0.026 and 0.043, respectively) had a reduced methylation in male newborns whose mother had preconception folic acid supplementation. Conclusion: DNA methylation changes in placenta tissues may be associated with SGA, maternal preconception folic acid supplementation status and also be fetal sex-specific.